Title: Protein-protein interaction investigated by steered molecular dynamics simulation

Speaker: Michel Cuendet - Olivier Michielin's Molecular Modeling Group, Swiss Institute of Bioinformatics

Date/Time: Thursday, November 20, 2008, 2:00 – 3:00 pm

Location: CSRI Building/Room 90 (Sandia-NM)

Brief Abstract: Molecular dynamic simulations offer the possibility to act on a system in ways that are experimentally unavailable.  For example, it allows to study in detail the interactions in a protein-protein complex by gradually forcing its dissociation in the course of a simulation.  The theory shows that binding free energy differences could be obtained from such nonequilibrium trajectories, provided that the temperature of the system is controlled in a proper way.  We present evidence and analyze the convergence difficulties encountered when applying the method to large systems.  A wealth of biologically important information can be extracted from the steered molecular dynamics simulations, including a detailed picture of the protein-protein interaction energies, hydrogen bonding patterns, or per-residue solvation effects.

CSRI POC: Anatole von Lilienfeld, (505) 284-8829